/*
 * Copyright (c) 2017 NCIC, Institute of Computing Technology, Chinese Academy of Sciences
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
 */
package org.ncic.bioinfo.sparkseq.algorithms.utils.fragments;

import java.util.Collection;
import java.util.Collections;
import java.util.List;

/**
 * Author: wbc
 */
public class FragmentCollection<T> {
    Collection<T> singletons;
    Collection<List<T>> overlappingPairs;

    public FragmentCollection(final Collection<T> singletons, final Collection<List<T>> overlappingPairs) {
        this.singletons = singletons == null ? Collections.<T>emptyList() : singletons;
        this.overlappingPairs = overlappingPairs == null ? Collections.<List<T>>emptyList() : overlappingPairs;
    }

    /**
     * Gets the T elements not containing overlapping elements, in no particular order
     *
     * @return
     */
    public Collection<T> getSingletonReads() {
        return singletons;
    }

    /**
     * Gets the T elements containing overlapping elements, in no particular order
     *
     * @return
     */
    public Collection<List<T>> getOverlappingPairs() {
        return overlappingPairs;
    }
}
